Tsunami-induced seawater inundation causes vertical seawater infiltration into coastal aquifers and induces unexpected salinization of fresh groundwater resources. Assessing future risks of seawater intrusion in tsunami-prone areas can provide essential information supporting disaster preparedness. In this study, we investigated seawater intrusion and aquifer recovery processes under the future Nankai earthquake and tsunami scenarios at Niijima Island, Japan. A groundwater model with a 2-D vertical cross section was developed to solve variable-density flow and salt transport in unsaturatedsaturated media using the numerical code, FEFLOW. Our simulation results indicate that the unsaturated zone behaves as an initial storage of the infiltrated seawater and controls the maximum amount of seawater infiltration during the anticipated tsunami inundation. The bedrock structures affect the direction of seawater movement in the saturated zone and the flushing time of the polluted aquifer. Our analysis suggests that the tsunami inundation height, the rainfall recharge rate, and hydraulic conductivity are the primary sources of uncertainties in the simulation results. These findings have implications for other tsunami-prone zones with respect to the understanding of the relevant physical processes and model uncertainties. Key Points: • Unsaturated zone initially stores infiltrated seawater during tsunami inundation and constrains the mass of infiltrated salt to subsurface • Bedrock structures affect the directions of seawater migration after tsunami inundation because of the contribution of density-driven flow • Tsunami inundation height, rainfall recharge rate, and hydraulic conductivity are the primary sources of model uncertainties Correspondence to: